The deal, set to be signed next week, was brokered only days after GPs in Merthyr Tydfil and Powys told GP that their LHBs were scrapping maternity locum pay altogether.
Under the minimum guarantee deal that comes into force in April, LHBs will fund 100 per cent of locum costs up to the maximum £1,500 weekly rate for the first eight weeks of maternity leave. For the subsequent 18 weeks, they will fund cover at half rate. The agreement is backed with £500,000 from the Welsh Assembly.
GPC Wales deputy chairman Dr David Bailey said: 'This is a recruitment plus point in Wales' favour.'
The deal is better than elsewhere in the UK. Under the GMS contract, primary care organisations are obliged to contribute to the cost of a locum for maternity cover, but the amount is discretionary.
Despite the agreement, Powys LHB has been accused of withdrawing all maternity cover payments by Newtown GP Dr Christopher Neill.
Powys LHB has denied the claim, saying that 'financial assistance is still made available to medical practices whose staff are away on maternity leave'.
Dr Nevill said: 'We know our LHB is struggling and this is the sort of area where it will get away with withdrawing payments.'
Dr Nevill's claim came only days after Dr Maria Cronje, a GP in Merthyr Tydfil, said her LHB decided that money to fund maternity, paternity or sick leave would be used to fund salaried GPs to cover leave.
Stephen Davies, assistant director of primary care at Merthyr Tydfil LHB, confirmed that a salaried service provided better continuity of care.
But if the practice did not accept the salaried GP, the board would fund locum cover 'within the financial entitlement', said Mr Davies.
The new maternity deal is not in the statement of financial entitlements for Wales, but it is set out in a circular that 'all LHBs are expected to comply with it', said Dr Bailey.
GPC Wales chairman Dr Andrew Dearden warned that he would expose defaulting LHBs.
'If any LHB breaks the agreement, I will publicly name and shame it in the local and national press,' he said. 'I might ask the Audit Commission for Wales how it took the money and did not distribute it.'